Well something strange happened. There i was playing my own mod, and all of a sudden out of nowhere i get this mission to annex Bohemia. So im all merry about it, and i proceed to kick some Czech butts, which naturally, goes exactly as i planned, and then i reach the point where i enforce peace demands. So, Bohemia owned 10 provinces + it had 5 Silesian vassals. My war score was 100% (everything occupied) and my total war cost for annexation was like 146% or whatever, so i couldnt take it all in just one go, Bohemia was reduced to 2 province minor + 5 vassals. Anyway, as soon as i peace out Poland and Maissen attach Bohemia, kick its butt, and force it to release Sorbia, effectively leaving it as one province minor (Prague) + 5 vassals. In the middle of that war i get scared so attack them despite truce, occupy everything again, only to find out to my astonishment that i cant annex Bohemia. Im thinking "well maybe its some kind of vassal thing", so i make them cancel all vassals which effectively reduces Bohemia to a OPM. Then i attack them again despite truce, and occupy their only province, and i still cant annex them.
So, since i checked, double checked and triple checked - there are no ghost provinces - the only other explanation that i can think of, is that being emperor prevents them from being annexed.
I am running version 5.2 and i would appreciate if someone could give me a definitive answer.